A week ago, Simon K, a 20-year-old student living in the capital of South Sudan, was arrested by men in military uniforms. He was asked a question that has taken on deadly importance in the world's newest country in the past seven days: incholdi – "What is your name?" in Dinka, the language of the country's president and its largest ethnic group.

Those who, like Simon, were unable to answer, risked being identified as Nuer, the ethnic group of the former vice-president now leading the armed opposition and facing the brunt of what insiders are describing as the world's newest civil war.

Simon K was taken to a police station in the Gudele market district of Juba, where he was marched past several dead bodies and locked in a room with other young men, all Nuer. "We counted ourselves and found we were 252," he told the Guardian. "Then they put guns in through the windows and started to shoot us."

The massacre continued for two days with soldiers returning at intervals to shoot again if they saw any sign of life. Simon was one of 12 men to survive the assault by covering themselves in the bodies of the dead and dying.

A displaced family from South Sudan's Nuer tribe, who fled their home in fear of ethnic killing by the Dinka-led government, erects a makeshift shelter inside the United Nations Mission in Sudan facility in Jabel. Photograph: James Akena/Reuters

Simon spoke from inside the UN compound that has become an emergency sanctuary to the remaining Nuer in the capital. Sitting on a filthy mattress by the side of a dirt road, with bandages covering bullet wounds in his stomach and legs, he recalled: "It was horrible, because to survive I had to cover myself with the bodies of dead people, and during the two days, the bodies started to smell really bad."

In the space of seven desperate days, the UN base has been transformed from a logistics hub for an aid operation into a squalid sanctuary for more than 10,000 people. Amid the confusion of bodies and belongings, a handmade sign hangs from the rolls of razor wire. "The lord is our best defender," it reads.

But there is no sign here of the lord's defence, as the country that gained independence in 2011 with huge international fanfare and support has come apart in the space of a week.

The latest violence began after a fight between Dinka and Nuer soldiers in the presidential guard on 15 December, igniting a simmering political power struggle in South Sudan's ruling party and sparking widespread ethnic killings.

Juba resident Gatluak Kual, who has bullet wounds in both arms and a prosthetic foot from the 20-year battle that split Sudan and created an independent south two years ago under President Salva Kiir, says the country is once more at war.

United Nations Mission in Sudan personnel guard South Sudanese people displaced by fighting in Jabel, on the outskirts of Juba, the South Sudan capital. Photograph: James Akena/Reuters

"Everyone here has lost someone [in the last week]," he said, gesturing out over the multitude with the finger he broke five days ago disarming a Dinka militiaman who was trying to kill him. "We have seen our daughters, our brothers, our mothers killed simply because they are Nuer. To me this is already a civil war."

The reverberations of the wave of targeted killings that began in the fledgling capital are being felt throughout the country, where they have sparked revenge attacks and copycat atrocities. Generals who have mutinied have seized the capital of South Sudan's largest state, Jonglei, and its main oil-producing area, Unity State. Former vice-president Riek Machar threw his support behind the armed opposition and is now its de facto leader. On Sunday a full-scale tank battle was being fought between opposing factions in the South's army in the far western reaches of oil-rich, swampy Upper Nile.

"It would have been difficult one week ago to imagine that things would unravel to this extent," said the UN's head of humanitarian affairs in South Sudan, Toby Lanzer.

The fighting has already claimed thousands, if not tens of thousands, of civilian lives. Hundreds of thousands of South Sudanese have fled into the bush or returned to home villages, according to the UN. The official death toll of 500, which corresponds with the number of dead in a single Juba hospital six days ago, is being dismissed by experts. A veteran aid worker, who has been assessing the scale and nature of the killings from sources nationwide, said the real figure was "in the tens of thousands".

On Monday, Machar claimed his forces had gained control of all the major oil fields in Unity and Upper Nile states. The information minister, Michael Makuei, told Reuters this was "wishful thinking".

In Juba, Gatwech T remembers how, last Tuesday, he ran for his life when soldiers attacked his home area of Hai Referendum. Some of the men outran the younger ones, who were caught by men in uniform. "They caught the boys and I stopped to watch. They counted them and there were 21 boys, as young as him," he said, pointing at a 15-year-old. "They tied their hands behind their backs and killed them."

Yien K, 28, was at home last Monday evening at around 10pm in the Jabarona area on the outskirts of the capital when he heard shooting. As it came closer he decided to hide at his brother's home. There were five of them inside the simple structure: his brother, his brother's wife, one-year-old niece and another six-year-old girl, a cousin. Yien recalls the moment just after midnight when the tracks of a tank ripped through the walls and crushed the one-year-old. "The tanks came and ran over the house," he said. "The men escaped but the woman and girls were killed."

Unlike some of Juba's neighbourhoods, which have divided along ethnic lines, Jabarona is a mixed area and Yien believes the tank operators had guides showing them where Nuer people were living.

In neighbourhoods such as Mangaten, Hai Referendum, Area 107 and Eden City, it is now easy to tell where the Nuer community lived. Halfway down the main market street of Mangaten, a dust-blown complex of tin-shack shops and rickety stalls, the bustle and activity stops. Most businesses have been ransacked, their rough shelves stripped of everything; stalls have been burned to the ground. Crossing into Hai Referendum, one of the highest density settlements in Juba, is now a ghost town of abandoned houses.

On Saturday, a few laid-back looters could be seen loading a meagre haul of plastic chairs, pots and foam mattresses on to three-wheelers. In some houses nearby plates of food were left behind, clothes have been scattered where people fled. Only broken plastic chairs, empty tubs of milk powder and smashed fans lie in the dirt.

UN peacekeepers distribute boxes of food to displaced people in South Sudan. Photograph: Anna Adhikari/AFP/Getty Images

Crossing the boundary into Eden City, the atmosphere changed. Plainclothes soldiers, one of them with a plastic-handled kitchen knife in the pocket of his shorts and a machete visible under his football shirt stopped and questioned any outsiders. Only 20 metres away was the charred corpse of a man lying with his legs splayed outside the looted Eden Sports bar.

Nearby, a nervous family had returned to their mud hut home, known as a tukul, to visit Moses' aged mother who is too ill to make the journey to the UN base less than a mile away. He was determined to leave before nightfall, when a dusk-to-dawn curfew imposed by the government begins. "The army is coming at night," he said. "You hear the guns going tuk-tuk-tuk."

Rose, who emerged from the tukul where Moses' mother is bed-ridden, said: "Everybody has been running because of war. We're also running."

South Sudan's government, which has received billions of dollars in foreign aid and is home to the largest UN peacekeeping operation in the world outside the Democratic Republic of Congo, continues to insist that massacres in Juba have not happened. The president, whose guards sparked the first fighting on 15 December, has assured the South Sudanese that his forces will protect civilians.

Philip Aguer, a spokesman for the Sudan People's Liberation Army, the civil war guerrilla force that is now the national army, denied any orchestrated attacks had taken place. He said he was unaware of the slaughter at Mangaten police station and blamed any deaths on "criminal elements" who had exploited the chance to loot and kill afforded by the crisis. "Even though some of these criminals are wearing army uniforms does not necessarily mean they are part of the army," he said. He denied any national army soldiers were involved: "No SPLA soldiers are involved in this criminal activity."

With regard to those carrying out the atrocities, he added: "We are ready to arrest them and take them to court."

But this description of rogue elements does not tally with the account of Riek W, who was until Saturday a serving member of the presidential guard, known to Jubans as the "Tigers".

A three-year veteran of the multi-ethnic unit that was meant to bind the diverse communities of what had been southern Sudan, he was not openly known as a Nuer to many of his colleagues and does not bear the traditional "Gaar" scarring that many Nuer men have on their faces.

Now in hiding in the UN base, he described how fighting between Dinka and Nuer members of the Tigers last Sunday night had spilled over into attacks on civilian Nuers all over the city.

"They took people who were not soldiers and tied their hands and shot them. I saw this with my own eyes, I was there wearing the same uniform as them."

Young men from the Dinka community, many of them with no military training, were given uniforms and guns from various armouries around the capital, including one located at President Kiir's own compound, known as J1, he says.

"It is soldiers who are doing this and militia from Dinka boys who have been given guns from the Tigers," he said.

Riek W said that his Dinka colleagues could not act without the authority of their commander and that they were "the same soldiers that are killing people at night".

Riek W, who decided to abandon his post in the president's compound at the weekend as he feared for his life and was horrified at the murder of civilians, said that the scale of the killings was being covered up. " They… are using the curfew to remove the bodies," he said.

He described how he had seen "large trucks" full of bodies, some of which were taken to grave sites dug with bulldozers, while others had been dumped in the river Nile at two points: one near the Bilpam barracks and one at Juba bridge. These reports have been corroborated by fishermen who have seen the bodies up on the river bank. "The numbers they are saying are completely wrong, people have been killed everywhere," Riek W said.

The Nuer who have survived in Juba, numbering 20,000, are now crammed into the city's two UN bases. Their fate is matched by another 14,000 civilians from other ethnic groups sheltering with the UN in South Sudan's other main towns.

Many of the Nuer crowded into the main UN mission base in Juba said they were sure the peacekeepers would protect them despite the evacuation over the weekend of all non-critical UN staff.

Not everyone feels safe, though. Wearing a dusty pinstriped suit jacket and apologising for not having showered in six days, 51-year-old Peter Bey was unsure. He has watched in recent days as one evacuation flight after another has taken foreign nationals to safety from the airport on the other side of the fence. "We see from history that the UN has left people behind before in Rwanda," he said. "They put their own people on helicopters and left the people who died."